Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1bc98dfcb617cf022070b96ee74f437cfe5c207 https://github.com/galaxyproject/galaxy/commit/d1bc98dfcb617cf022070b96ee74f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M contrib/galaxy_config_merger.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/model/__init__.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/jstree.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/library_upload_dir.py M scripts/api/workflow_import.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/extract_toolbox_sections.py M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tools.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/update_shed_config_path.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py Log Message: ----------- Python3: fix remaining print statements Remove some debugging prints. Fix import order. Consolidate exception logging in ToolShed database migrations. Commit: 73b4629a0be4956da976e0e7758f8b189c485821 https://github.com/galaxyproject/galaxy/commit/73b4629a0be4956da976e0e7758f8... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M contrib/galaxy_config_merger.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/model/__init__.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/jstree.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/library_upload_dir.py M scripts/api/workflow_import.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/extract_toolbox_sections.py M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tools.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/update_shed_config_path.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py Log Message: ----------- Merge pull request #4799 from nsoranzo/python3 Python3: fix remaining print statements Compare: https://github.com/galaxyproject/galaxy/compare/16843cee9ac2...73b4629a0be4